This is a repository copy of Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/81059/ Version: Published Version Article: Rainford, James Lewis, Hofreiter, Michael, Nicholson, David Blair et al. (1 more author) (2014) Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects. PLoS ONE. e109085. ISSN 1932-6203 https://doi.org/10.1371/journal.pone.0109085 Reuse Items deposited in White Rose Research Online are protected by copyright, with all rights reserved unless indicated otherwise. They may be downloaded and/or printed for private study, or other acts as permitted by national copyright laws. The publisher or other rights holders may allow further reproduction and re-use of the full text version. This is indicated by the licence information on the White Rose Research Online record for the item. Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Phylogenetic Distribution of Extant Richness Suggests Metamorphosis Is a Key Innovation Driving Diversification in Insects James L. Rainford1*, Michael Hofreiter1,2, David B. Nicholson1,3,4, Peter J. Mayhew1 1 Department of Biology, University of York, York, United Kingdom, 2 Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany, 3 Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom, 4 Department of Earth Sciences, The Natural History Museum, London, United Kingdom Abstract Insects and their six-legged relatives (Hexapoda) comprise more than half of all described species and dominate terrestrial and freshwater ecosystems. Understanding the macroevolutionary processes generating this richness requires a historical perspective, but the fossil record of hexapods is patchy and incomplete. Dated molecular phylogenies provide an alternative perspective on divergence times and have been combined with birth-death models to infer patterns of diversification across a range of taxonomic groups. Here we generate a dated phylogeny of hexapod families, based on previously published sequence data and literature derived constraints, in order to identify the broad pattern of macroevolutionary changes responsible for the composition of the extant hexapod fauna. The most prominent increase in diversification identified is associated with the origin of complete metamorphosis, confirming this as a key innovation in promoting insect diversity. Subsequent reductions are recovered for several groups previously identified as having a higher fossil diversity during the Mesozoic. In addition, a number of recently derived taxa are found to have radiated following the development of flowering plant (angiosperm) floras during the mid-Cretaceous. These results reveal that the composition of the modern hexapod fauna is a product of a key developmental innovation, combined with multiple and varied evolutionary responses to environmental changes from the mid Cretaceous floral transition onward. Citation: Rainford JL, Hofreiter M, Nicholson DB, Mayhew PJ (2014) Phylogenetic Distribution of Extant Richness Suggests Metamorphosis Is a Key Innovation Driving Diversification in Insects. PLoS ONE 9(10): e109085. doi:10.1371/journal.pone.0109085 Editor: Axel Janke, BiK-F Biodiversity and Climate Research Center, Germany Received July 9, 2014; Accepted September 8, 2014; Published October 2, 2014 Copyright: ß 2014 Rainford et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files. Funding: The study was primarily funded by NERC (http://www.nerc.ac.uk) grant NE/J500197/1. Contributions were also made by the National Museums of Scotland and The Natural History Museum, London in funding for DN. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * Email: [email protected] Introduction tions, notably the evolution of flowering plants (angiosperms) [10– 12] and parasitism [13]. Hexapoda, including insects and their six-legged relatives, are Attempts to explicitly test these ideas within a phylogenetic the most species-rich animal clade in terrestrial ecosystems and framework have either been restricted to particular orders [14– collectively comprise over half of all described extant species [1,2]. 16], thus omitting a wider context, or have ignored variation Therefore understanding the origins of this exceptional richness is within orders [7,8]. Here we integrate these disparate approaches key to understanding the history of life on land and the assembly of by producing a dated hypothesis of phylogenetic relationships terrestrial ecosystems [3]. In addition to their high overall species across the hexapods that is near-complete at the family level, richness, insect groups are also remarkable for the degree of through the combination of previously published molecular disparity in richness existing among the major sub-clades. For sequence data and a set of literature derived constraints (see example the orders Zoraptera (‘‘angel insects’’) and Coleoptera below and Supplementary materials). Our goal is therefore not to (beetles) differ in richness by four orders of magnitude (32 and present a novel estimate of the hexapod phylogeny (see discussion 350,000 described extant species, respectively [2]). A key part of below), but instead to focus on what current taxonomic, the discussion on these differences in extant richness relates to the phylogenetic and paleontological evidence reveals about broad hypothesized effects of potential key innovations that may have patterns of diversification within the group, and its relationship acted as drivers for hexapod richness [3]. Such proposed with key evolutionary innovations, environmental changes and innovations include both major morphological developments mass extinctions [17–19]. including the origin of the insect body plan [2–4], flight [2–6], the capacity to fold the wings [7,8] and the origin of complete metamorphosis [2–4,9], and ecological opportunities or innova- PLOS ONE | www.plosone.org 1 October 2014 | Volume 9 | Issue 10 | e109085 Diversification of Extant Insects: Metamorphosis Is a Key Innovation Figure 1. Dated phylogeny of extant hexapod families showing diversification rate shifts. The tree shown is from a maximum likelihood analysis of 8 genes, calibrated by 89 fossils. Membership of major clades is denoted by coloration of the ring (grey: Entognatha, black: basal insects, cyan: Palaeoptera, magenta: Polyneoptera, green: Paraneoptera, red: Holometabola). Changes in branch coloration denote diversification shifts identified using TurboMEDUSA (Table S3). Branch colors identify regions of the tree with the same underlying diversification model. Symbols at shifts denote a net upshift (diamond) or down shift (circle). Coloration of symbols reflects the robustness of the shift event across 500-scaled samples taken from the post-burin MCMC chain (black: shift recovered in .80% of samples, grey with black outline: recovery .50%, grey with pale outline: recovery .30%, pale grey: recovery,30%). Black rings are shown at 100 Ma increments from the present. See Supplementary materials for further details and discussion. See also Figures S1–S3, Tables S1–S4, and Datafiles S1, S2. doi:10.1371/journal.pone.0109085.g001 Results certain widely recognized phylogenetic nodes ([20,21] see Sup- plementary materials for details). The tree topology was inferred The dated phylogeny used in this study contains 874 higher taxa using a partitioned RAxML (maximum likelihood) analysis of Hexapoda (Fig. 1). Taxa were variously resolved to family or [22,23]. This topology was dated using a relaxed molecular clock superfamily level, such that the presented tree incorporates a total implemented in MrBayes 3.2 [24] and calibrated using 86 fossil of 903 of the approximately 1100 recognized extant families, with dates taken from the recent palaeoentomological literature (Table taxonomy following that given by GenBank references up to S2). August 2013 (see Supplementary materials for further discussion). Using our dated tree we estimated the crown divergence of The tree was reconstructed using a combination of eight widely Hexapoda, i.e. the divergence of true insects from Entognatha sampled molecular markers and literature-derived constraints on (basal hexapods including springtails) as occurring in the PLOS ONE | www.plosone.org 2 October 2014 | Volume 9 | Issue 10 | e109085 Diversification of Extant Insects: Metamorphosis Is a Key Innovation Figure 2. Lineage (y-axis; log scale) through time (x-axis; Ma) plot for the major groups of Hexapoda using the phylogeny in Fig. 1. Colors used identify the same clades as the ring in Fig. 1. Thick lines